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TitleA Nucleosome Bridging Mechanism for Activation of a Maintenance DNA Methyltransferase.
Journal, issue, pagesMol. Cell, Vol. 73, Issue 1, Page 73-83.e6, Year 2019
Publish dateJan 3, 2019
AuthorsCaitlin I Stoddard / Suhua Feng / Melody G Campbell / Wanlu Liu / Haifeng Wang / Xuehua Zhong / Yana Bernatavichute / Yifan Cheng / Steven E Jacobsen / Geeta J Narlikar /
PubMed AbstractDNA methylation and H3K9me are hallmarks of heterochromatin in plants and mammals, and are successfully maintained across generations. The biochemical and structural basis for this maintenance is ...DNA methylation and H3K9me are hallmarks of heterochromatin in plants and mammals, and are successfully maintained across generations. The biochemical and structural basis for this maintenance is poorly understood. The maintenance DNA methyltransferase from Zea mays, ZMET2, recognizes dimethylation of H3K9 via a chromodomain (CD) and a bromo adjacent homology (BAH) domain, which flank the catalytic domain. Here, we show that dinucleosomes are the preferred ZMET2 substrate, with DNA methylation preferentially targeted to linker DNA. Electron microscopy shows one ZMET2 molecule bridging two nucleosomes within a dinucleosome. We find that the CD stabilizes binding, whereas the BAH domain enables allosteric activation by the H3K9me mark. ZMET2 further couples recognition of H3K9me to an increase in the specificity for hemimethylated versus unmethylated DNA. We propose a model in which synergistic coupling between recognition of nucleosome spacing, H3K9 methylation, and DNA modification allows ZMET2 to maintain DNA methylation in heterochromatin with high fidelity.
External linksPubMed:30415948 / Publisher's page
KeywordsAnimals / DNA Methylation / DNA Modification Methylases / Enzyme Activation / Escherichia coli / Microscopy, Electron / Models, Molecular / Nucleic Acid Conformation / Nucleosomes / Plant Proteins / Protein Binding / Protein Interaction Domains and Motifs / Structure-Activity Relationship / Substrate Specificity / Xenopus laevis / ZMET2 protein, Zea mays
MethodsEM (single particle)
Resolution28 A
Structure data

EMDB-9127:
A nucleosome bridging mechanism for activation of a maintenance DNA methyltransferase

Source
  • Xenopus laevis (African clawed frog)
  • Zea mays (maize)
  • synthetic construct (others)

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